Research workbench
Putative methyltransferase yhhf from escherichia COLI.
Analyse Putative methyltransferase yhhf from escherichia COLI. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FPO
- Type
- protein
- Length
- 1,070 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylase yhhf
- EC
- 2.1.1.-
- UniProt
- P0ADX9
- Ligands
- CL
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylase yhhf (EC 2.1.1.-) | protein | 177 | 32% helix, 31% strand | P0ADX9 |
| B, E | Methylase yhhf (EC 2.1.1.-) | protein | 178 | 29% helix, 31% strand | P0ADX9 |
| C | Methylase yhhf (EC 2.1.1.-) | protein | 181 | 27% helix, 31% strand | P0ADX9 |
| D | Methylase yhhf (EC 2.1.1.-) | protein | 179 | 32% helix, 31% strand | P0ADX9 |
| F | Methylase yhhf (EC 2.1.1.-) | protein | 177 | 27% helix, 31% strand | P0ADX9 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.73 | 0.82 | 56 | empty |
| 2 | 545 | 0.70 | 0.79 | 49 | empty |
| 3 | 507 | 0.68 | 0.79 | 49 | empty |
| 4 | 499 | 0.67 | 0.78 | 54 | empty |
| 5 | 479 | 0.61 | 0.75 | 57 | empty |
Interfaces
5 interfaces between chains.
- E–F · 880 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 865 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 856 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 820 Ų buried · 13 hydrogen bonds · protein-protein
- C–F · 350 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2FPO · Putative methyltransferase yhhF from Escherichia coli. · the same entry in another collection · chain F against F, TM-score 1.00
- P0ADX9 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase D… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0ADX9
- Elsewhere: RCSB PDB 2FPO · PDBe 2FPO · UniProt P0ADX9
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